Metadata-Version: 1.2
Name: bioservices
Version: 1.7.6
Summary: Access to Biological Web Services from Python
Home-page: http://github.com/cokelaer/bioservices
Author: Thomas Cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: GPLv3
Download-URL: http://pypi.python.org/pypi/bioservices
Description: BioServices
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        .. image:: https://badge.fury.io/py/bioservices.svg
            :target: https://pypi.python.org/pypi/bioservices
        
        .. image:: https://secure.travis-ci.org/cokelaer/bioservices.png
            :target: http://travis-ci.org/cokelaer/bioservices
        
        .. image:: https://coveralls.io/repos/cokelaer/bioservices/badge.png?branch=master
           :target: https://coveralls.io/r/cokelaer/bioservices?branch=master
        
        .. image:: http://readthedocs.org/projects/bioservices/badge/?version=master
            :target: http://bioservices.readthedocs.org/en/master/?badge=master
            :alt: Documentation Status
        
        
        :Python_version_available: BioServices is tested for Python 2.7, 3.6, 3.7
        :Contributions: Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/
        :Issues: Please use https://github.com/cokelaer/bioservices/issues
        :How to cite: Cokelaer et al. *BioServices: a common Python package to access biological Web Services programmatically*
             `Bioinformatics <http://bioinformatics.oxfordjournals.org/content/29/24/3241>`_ (2013) 29 (24): 3241-3242
        :Documentation: `RTD documentation <http://bioservices.readthedocs.io/>`_.
        
        **Bioservices** is a Python package that provides access to many Bioinformatices Web Services (e.g.,
        UniProt) and a framework to easily implement Web Services wrappers (based on 
        WSDL/SOAP or REST protocols).
        
        .. image:: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
            :target: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
        
        
        The primary goal of **BioServices** is to use Python as a glue language to provide
        a programmatic access to several Bioinformatics Web Services. By doing so, elaboration of  new
        applications that combine several of the wrapped Web Services is fostered.
        
        One of the main philosophy of **BioServices** is to make use of the existing
        biological databases (not to re-invent new databases) and to alleviates the
        needs for expertise in Web Services for the developers/users.
        
        BioServices provides access to 25 Web Services including. For a quick start,
        look at some notebooks here `github cokelaer/bioservices <https://github.com/cokelaer/bioservices/tree/master/notebooks/>`_ and here `github bioservices <https://github.com/bioservices/notebooks>`_.
        
        An up-to-date list of Web Services is provided within 
        the online `documentation <http://http://bioconvert.readthedocs.io/>`_.
        
        Here is a small example using the UniProt Web Service to search for the zap70 specy in human
        organism::
        
            >>> from bioservices import UniProt
            >>> u = UniProt(verbose=False)
            >>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, 
            ...                 columns="entry name,length,id, genes")
            >>> print(data)
            Entry name   Length  Entry   Gene names
            ZAP70_HUMAN  619     P43403  ZAP70 SRK
            B4E0E2_HUMAN 185     B4E0E2
            RHOH_HUMAN   191     Q15669  RHOH ARHH TTF
        
        More examples and tutorials are available in the exhaustive 
        `On-line documentation <http://bioconvert.readthedocs.io/>`_
        
        
        
        
        Release History
        ------------------
        This is a summary of the changelog. Complete change can be found in the 
        `main documentation <http://bioconvert.readthedocs.io/en/master/ChangeLog.html>`_.
        
        
        
        Revision 1.7.0
        --------------
        
        * General fixes and update from @thobalose (https://github.com/cokelaer/bioservices/pull/149) to
          updating matplotlib to 3.0.3
        * added  panther module (pantherdb.org)
        * added tests for pubchem, pfam and eva modules, which are still in draft version though
        * deprecated PICR and TCGA modules (the latter was not really available anyway)
        * Fixed wikipathway, kegg, reactome tests and code (issues 148 and 151)
        
        
        1.6.X
        -----
        
        * rewrote entirely the ChEMBL wrapper due to new ChEMBL API.
        * removed the quickgo_old module and its tests
        * Fix typo for a "valid colum," in uniprot module
        * Changed biomodels WSDL endpoint (thanks to https://github.com/thobalose. )
        * uses colorlog to have more robust and consistent logging.
        * Fixed wikipathway XML issues by outputing dictionaries now. This fixes 
              https://github.com/cokelaer/bioservices/issues/131
        * Fix https://github.com/cokelaer/bioservices/issues/137 to handle KEGG GENE
          field properly in KEGGParse
        * Fix https://github.com/cokelaer/bioservices/issues/125 thanks to 
              https://github.com/thobalose. 
        
        
        1.5.X
        ---------
        
        * Support for Python 3.6 on Travis.
        * No more support for Python 2.6
        * biodbnet and wikipathways services now uses the REST protocol (instead of WSDL).
        * move readseq to seqret and uses new EBI API
        * move wsdbfetch to dbfetch (and switch to  REST protocol)
        * quickgo uses the new API from EBI
        * New Reactome API
        * For developers: use pytest instead of nosetests.
        
        
        
        
        1.4.X
        ---------------
        
        * Update uniprot valid column names.
        * Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
        * Replaced deprecated HGNC with the official web service from genenames.org
        * Fully updated EUtils since WSDL is now down; implementation uses REST now.
        * Removed the apps/taxonomy module now part of http://github.com/biokit. 
        * added http_delete in services.py
        
        
        
        
        
        1.3.X
        +++++++++++
        
        * Source code moved to github.com
        * New REST class to use **requests** package instead of urllib2. 
        * Creation of a global configuration file in .config/bioservice/bioservices.cfg
        * NEW services: Reactome, Readseq, Ensembl, EUtils, PRIDE, clinvitae, Intact
          (complex)
        * CHANGES: all parameters called format have been renamed frmt (to avoid using Python keyword)
        
        1.2.X
        +++++++++++
        
        * add try/except for pandas library.
        * added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
        * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf
        
        1.1.X
        +++++++++++ 
        * NEW services: biocarta, pfam, ChEBI, UniChem
        * Add documentation and examples related to Galaxy/BioPython.
        * NEW Service : HGNC
        * Use BeautifulSoup4 instead of 3
        
        1.0.X
        +++++++++++ 
        * add PDB, ArrayExpress,  biomart, chemspider draft, eutils, miriam, arrayexpress 
        
        1.0.0
        ++++++
        
        * First release of bioservices including the following services:
          BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
          WSDbfetch, NCBIblast, PSICQUIC, Wikipath
        
        
        
        Release History
        ------------------
        This is a summary of the changelog. Complete change can be found in the 
        `<main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.
        
        
        
        
        1.4.X
        ---------------
        
        * Include RNASEQ (EBI) in module rnaseq_ebi
        * Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
        * Replaced deprecated HGNC with the official web service from genenames.org
        * Fully updated EUtils since WSDL is now down; implementation uses REST now.
        * Removed the apps/taxonomy module now part of http://github.com/biokit. 
        * added http_delete in services.py
        
        
        
        1.3.X
        +++++++++++
        
        * CACHE files are now stored in a general directory in the home, rather than
          locally
        * Source code moved to github.com
        * New REST class to use **requests** package instead of urllib2. 
        * Creation of a global configuration file in .config/bioservice/bioservices.cfg
        * NEW services: Reactome, Readseq, Ensembl, EUtils
        
        1.2.X
        +++++++++++
        
        * add try/except for pandas library.
        * added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
        * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf
        
        1.1.X
        +++++++++++ 
        * NEW services: biocarta, pfam, ChEBI, UniChem
        * Add documentation and examples related to Galaxy/BioPython.
        * NEW Service : HGNC
        * Use BeautifulSoup4 instead of 3
        
        1.0.X
        +++++++++++ 
        * add PDB, ArrayExpress,  biomart, chemspider draft, eutils, miriam, arrayexpress 
        
        1.0.0:
        +++++++++++ 
        * First release of bioservices
        
        
        0.9.X: 
        +++++++++++ 
        * Stable version of bioservices including the following services:
        	BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
        	WSDbfetch, NCBIblast, PSICQUIC, Wikipath
        
        
Keywords: BioServices,WebServices,Biology,BioDBNet,ChEBI,UniChem,Kegg,KEGG,BioModels,EUtils,UniProt,PICR,ArrayExpress,MUSCLE,QuickGO,PDB,PSICQUIC,Blast,BioMART,BioGRID,MIRIAM,BioMart,GeneProf,ChEMBL,ChemSpider,HGNC,PathwayCommons,Rhea,Ensembl
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
